SSIS - SCD Type 1 - Output - how to handle rows deleted in source?

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I have an SSIS package that handles synchronization between two databases.

After we did an audit - as users complained the data reported by the two systems (that are separate AF) differs between the two - and we found a number of issues. Biggest one was that in some tables there were rows that did not exist in source for that sync. They were deleted by some user, disregarding basically every protocol for data handling. QC people were not amused.

But the damage is done. Now, how do I handle this? It literally means that those records fell through the cracks: they are in my DB, they are flagged as active rows (but they are most definitely not active), they will not be matched with anything in the input, thus they will never become inactive.

I hoped I can Output them somehow from the SCD, but I get an error when trying to do anything with that SCD.

But That's just part of the problem - first I need to make them part of the process again, so that if it ever happens at least There will be some message to someone, who can then investigate.

What would be the best practice to handle that mess? Or just update them manually and hope the sync will pick them up in later stages and update other data based on them in due process? enter image description here

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